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Purpose: Retinoblastomas are malignant eye tumors diagnosed in young children. Most retinoblastomas are genetically characterized by biallelic inactivation of the RB1 gene. However, 1.5% of tumors demonstrate high-level amplification of the proto-oncogene MYCN. Patients with MYCN-amplified RB1-proficient retinoblastoma receive a diagnosis at an earlier age and show a clinically and histologically more malignant phenotype. This study aimed to identify genome-wide molecular features that distinguish this subtype from other retinoblastomas. Design: Cohort study. Participants: Forty-seven retinoblastoma tumors, comprising 36 RB1–/–, 4 RB1+/–, and 7 RB1+/+ tumors. In total, 5 retinoblastomas displayed high-level MYCN amplification, with 3 being RB1+/+, 1 being RB1+/–, and 1 being RB1–/–. Methods: Integrated analysis, based on gene expression, methylation, and methylation-expression correlations, was performed to identify distinct molecular components of MYCN-amplified RB1-proficient retinoblastomas compared with other retinoblastoma subtypes. The methylation and methylation-expression correlation analysis was initially conducted within a subset of samples (n = 15) for which methylation profiles were available. The significant findings were cross-validated in the entire cohort (n = 47) and in publicly available data. Main Outcome Measures: Differentially expressed genes/pathways, differentially methylated genes, and methylation-driven differential gene expression. Results: A large number of genes (n = 3155) were identified with distinct expression patterns in MYCN-amplified RB1-proficient retinoblastomas. The upregulated and downregulated genes were associated with translation and cell-cycle processes, respectively. Methylation analysis revealed distinct methylated patterns in MYCN-amplified RB1-proficient tumors, many of which showing significant impact on gene expression. Data integration identified a 40-gene expression signature with hypermethylated state resulting in a significant downregulation in MYCN-amplified RB1-proficient retinoblastomas. Cross-validation using the entire cohort and the public domain expression data verified the overall lower expression of these genes not only in retinoblastomas with a MYCN-amplified RB1-proficient background, but also in MYCN-amplified neuroblastomas. These include the metabolism-associated TSTD1 gene and the cyclin-dependent kinase inhibitor gene CDKN2C. Conclusions: MYCN-amplified RB1-proficient retinoblastomas display significantly distinct molecular features compared with other retinoblastomas, including a set of 40 hypermethylation-driven downregulated genes. This gene set can give insight into the biology of MYCN-amplified retinoblastomas and may help us to understand the more aggressive clinical behavior.

DNA methylation (5mC) and hydroxymethylation (5hmC) are chemical modifications of cytosine bases which play a crucial role in epigenetic gene regulation. However, cost, data complexity and unavailability of comprehensive analytical tools is one of the major challenges in exploring these epigenetic marks. Hydroxymethylation-and Methylation-Sensitive Tag sequencing (HMST-seq) is one of the most cost-effective techniques that enables simultaneous detection of 5mC and 5hmC at single base pair resolution. We present HMST-Seq-Analyzer as a comprehensive and robust method for performing simultaneous differential methylation analysis on 5mC and 5hmC data sets. HMST-Seq-Analyzer can detect Differentially Methylated Regions (DMRs), annotate them, give a visual overview of methylation status and also perform preliminary quality check on the data. In addition to HMST-Seq, our tool can be used on whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data sets as well. The tool is written in Python with capacity to process data in parallel and is available at (https://hmst-seq.github.io/hmst/).

Prunella vulgaris (PV) is a medicine and food homologous plant, but its quality evaluation seldom relies on the polysaccharides (PVPs). In this work, we established the multi-level fingerprinting and in vitro anti-inflammatory evaluation approaches to characterize and compare the polysaccharides of P. vulgaris collected from the major production regions in China. PVPs prepared from 22 batches of samples gave the content variation of 5.76-24.524 mg/g, but displayed high similarity in the molecular weight distribution. Hydrolyzed oligosaccharides with degrees of polymerization 2-14 were characterized with different numbers of pentose and hexose by HILIC-MS. The tested 22 batches of oligosaccharides exhibited visible differences in peak abundance, which failed to corelate to their production regions. All the PVPs contained Gal, Xyl, and Ara, as the main monosaccharides. Eleven batches among the tested PVPs showed the significant inhibitory effects on NO production on LPS-induced RAW264.7 cells at 10 μg/mL, but the exerted efficacy did not exhibit correlation with the production regions. Conclusively, we, for the first time, investigated the chemical features of PVPs at three levels, and assessed the chemical and anti-inflammatory variations among the different regions of P. vulgaris samples., Competing Interests: Declaration of competing interest We declare that, we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled, “Multi-level chemical characterization and anti-inflammatory activity evaluation of the polysaccharides from Prunella vulgaris”., (Copyright © 2024. Published by Elsevier B.V.)

Interests in the development and exploration of industrial applications of medicinal mushrooms as postbiotics have lately increased. We recently reported the potential use of Phellinus linteus mycelial-containing whole culture extract (PLME) prepared by submerged cultivation as a postbiotic that promotes immune system activation. Here, we aimed to isolate and structurally elucidate the active ingredients in PLME by activity-guided fractionation. The intestinal immunostimulatory activity was evaluated by bone marrow (BM) cell proliferation activity and related cytokine production in C3H-HeN mouse-derived Peyer's patch (PP) cells treated with polysaccharide fractions. The initially crude polysaccharide (PLME-CP) of PLME prepared using ethanol precipitation was further fractionated into four fractions (PLME-CP-0 to -III) by anion-exchange column chromatography. BM cell proliferation and cytokine production of PLME-CP-III were significantly improved compared to those of PLME-CP. PLME-CP-III was then fractionated into PLME-CP-III-1 and PLME-CP-III-2 by gel filtration chromatography. Based on the molecular weight distribution, monosaccharide, and glycosyl linkage analyses, PLME-CP-III-1 was revealed as a novel galacturonic acid-rich acidic polysaccharide and further shown to play an important role in facilitating PP-mediated intestinal immunostimulatory activity. This is the first study demonstrating the structural characteristics of a novel intestinal immune system modulating acidic polysaccharide from P. linteus mycelium-containing whole culture broth postbiotics., Competing Interests: Declaration of competing interest The authors declare that they have no competing interests., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Long-term and excessive herbicide use has led to some environmental concerns and especially, herbicide resistance evolution in weeds. Here, we confirmed acetolactate synthase (ALS) inhibiting herbicide penoxsulam resistance and cross resistance to acetyl-coenzyme carboxylase (ACCase) inhibiting herbicides (cyhalofop-butyl and metamifop) in a global weed Echinochloa crus-galli population resistant to these herbicides (R). Penoxsulam metabolism study indicated that degradation rate was significantly higher in R than susceptible E. crus-galli population (S). RNA-sequencing revealed that a cytochrome P450 (P450) gene, CYP81A68, expressed higher in R versus S. Rice seedlings overexpressing this CYP81A68 gene are resistant to penoxsulam, cyhalofop-butyl and metamifop, and penoxsulam resistance is due to enhanced metabolism via O-demethylation. Deletion analysis of the CYP81A68 gene promoter identified an efficient region, in which differential methylation of CpG islands occurred between R and S. Collectively, these results demonstrate that upregulation of E. crus-galli CYP81A68 gene endows generalist metabolic resistance to commonly used ALS- and ACCase-inhibiting herbicides in rice fields and epigenetic regulation may play a role in the resistance evolution. This research could contribute to strategies reducing herbicide environmental impacts by judicious selection of alternative herbicide and non-chemical control tactics., (Copyright © 2022 Elsevier B.V. All rights reserved.)

An arabinan-rich acidic polysaccharide, named ALP4-2 ([α]20 D = +197.8 (c 1.0 mg/mL, H 2 O); and M w  = 5.59 × 10 3  g/mol), was obtained from Atractylodes lancea (Thunb.) DC. ALP4-2 is mainly comprised of Ara along with a small amount of GalA, Gal, Rha, Glc and Xyl. The structure was decorated by glycosidic linkages of α-Araf-(1→, →3)-α-Araf-(1→, →5)-α-Araf-(1→, →3,5)-α-Araf-(1→, →2,4)-α-Rhap-(1→, α-GalAp-(1→, →4)-α-GalAp-6-OMe-(1→, →4)-α-GalAp-6-OMe and β-Galp-(1→ with a ratio of 6:1:7:5:5:1:7:1:4. The structure, configuration and microstructure of ALP4-2 was proposed by comprehensive considerations of results from SEC-MALLS-RID, SEC-HRMS, GC-MS, and 1D/2D NMR spectroscopy. Except for a high methyl ester in full pectin regions, an abundant arabinan moiety is observed in ALP4-2 with highly complex and branched characteristics. The immunoactivity displayed that ALP4-2 can significantly promote phagocytosis of macrophage without cytotoxicity, and stimulate nitric oxide and cytokines (TNF-α, IL-6 and IL-10) release on RAW 264.7., (Copyright © 2021 Elsevier B.V. All rights reserved.)

A water-soluble acidic polysaccharide (AOP-2) from Althaea officinalis L. root was isolated by water extraction and purified by ion exchange chromatography (Cellulose DEAE-52) and gel filtration (Sephadex G-200). The structure characteristics of AOP-2 was determined by gel permeation chromatography (GPC), high performance liquid chromatography (HPLC), fourier transform infrared (FT-IR), nuclear magnetic resonance (NMR) spectrum and gas chromatography-mass spectrometry (GC_MS). The results indicated that the AOP-2 was an acidic hetropolysaccharide with the molecular weight of 639.27 kDa. The AOP-2 composed of 51% galacturonic acid, 32.56% rhamnose, 12.73% glucose and 3.71% galactose. It could be found that the main backbone chain of AOP-2 consisted of →3)-α-D-GalpA-(1→, →3)-α-D-Rhap-(1→ and→3,4)-β-D-Galp-(1→ with branches of →4)-α-D-Rhap-(1→, →4)-α-D-Glcp-(1→ and α-D-Rhap-(1 → . Thermal analysis revealed that the AOP-2 had high thermal stability and according to the results obtained from XRD analysis, it had a semi-crystalline structure. The results of Steady-shear flow and dynamical viscoelasticity showed that AOP-2 solutions exhibited shear-thinning behavior with high viscosity and a weak gel-like behavior at concentrations above 1% in linear viscoelastic region. In addition, it showed relatively high antioxidant property., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Hyperlipidemia is one major cause of atherosclerosis, which is a basic pathological change of cardiovascular diseases. Polysaccharide is a water-soluble component with lipid-lowering effects. In this study, alkaline-extracted polysaccharides were obtained from the fruiting body of C. militaris. Polysaccharides were purified via anion exchange and size exclusion chromatography. Their structural characteristics were investigated via chemical and spectroscopic methods. CM3I was mainly composed of →4)α-D-Glcp(1 → glycosyls and differed from starch due to the presence of →4,6)β-D-Glcp(1 → glycosyls. CM3II was characterized by its backbone, which was composed of →4)-β-D-Manp(1 → 6)-α-D-Manp(1 → 6)-β-D-Manp(1 → linked glycosyls, and especially the presence of O-methyl. Moreover, CM3II exhibited powerful anti-atherosclerotic effects via lowering plasma lipid levels in apolipoprotein E-deficient mice. The underlying mechanisms were attributed to its promoting effect on LXRα and inhibitory effect on SREBP-2. Collectively, CM3I and CM3II are different from the previously reported polysaccharides from C. militaris, and CM3II has a potential application in hypolipidemia and anti-atherosclerosis., Competing Interests: Declaration of competing interest None., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Sedum sarmentosum Bunge (SS) is clinically used as Chinese medicine for hepatitis related diseases treatment. The purpose of this study was to explore the chemical structures of polysaccharides from this plant. A neutral polysaccharide (SSWP) was isolated and purified by ion-exchange chromatography and Superdex-75 column. The obtained SSWP was a homogenous one with a molecular weight of 21.5 kDa according to the high-performance gel permeation chromatography. The major monosaccharide composition of SSWP was arabinose, glucose and galactose in a molar ratio of 2.4:1:1.8. The methylation analysis showed that SSWP consists mainly of Araf-(1→, →5)-Araf-(1→, →3,5)-Araf-(1→, →4)-Galp-(1→, →4)-Glcp-(1→. The NMR result and enzymatic digestion data comprehensively indicated that SSWP was a novel arabinogalactoglucan-type structure. The anticancer assay in vitro exhibited that SSWP could effectively inhibit 48.9% of Huh-7 cells growth at 50 μg/mL and arrest cells at S-phase, and induce tumor cells apoptosis. Together, polysaccharide from S. sarmentosum Bunge could be a potential natural antitumor agent., Competing Interests: Declaration of competing interest All authors declare no conflicts of interest., (Copyright © 2021 Elsevier B.V. All rights reserved.)

One novel alkali-extracted polysaccharide, CM3-SII, was obtained from the fruiting body of C. militaris via column chromatography. Its structural characteristics were investigated via chemical and spectroscopic methods. The backbone of CM3-SII was composed of →4)-β-D-Manp(1→, →6)-β-D-Manp(1→, and →6)-α-D-Manp(1→ glycosyls, and branching at the O-4 positions of →6)-β-D-Manp(1→ glycosyls with β-D-Galp, (1→2) linked-β-D-Galf, and →2,6)-α-D-Manp(1→ residues. Furthermore, O-6 and O-2 positions of the →2,6)-α-D-Manp(1→ residues were substituted with methyl and β-D-Galp, respectively. This polysaccharide significantly enhanced the intracellular protein expression of low-density lipoprotein receptor and proprotein convertase subtilisin/kexin type 9 (PCSK9) via regulating sterol regulatory element-binding protein 2 in hepatoma Huh7 cells. Of note, CM3-SII significantly decreased PCSK9 secretion at the concentration of 200 μg/mL. Collectively, CM3-SII is different from the previously reported alkali-extracted polysaccharides isolated from the fruiting body of C. militaris, and it may have potential application in hypolipidemia or as a pharmaceutical additive., Competing Interests: Declaration of competing interest None., (Copyright © 2021 Elsevier B.V. All rights reserved.)

In this study, a new strain suspected to be Aureobasidium pullulans was isolated from trees leaves. The molecular characterization and the resulting phylogenetic tree showed that the isolated strain was A. pullulans. Also, the results of methylation analysis, monosaccharide composition, FTIR, NMR and XRD confirmed that the obtained exo-polysaccharide from the mentioned strain was pullulan. The pullulan production optimization by central composite design (CCD) indicated that the maximum yield obtained under optimum conditions (pH of 6.5, sucrose concentration of 5.5% (w/v) and yeast extract concentration of 0.1% (w/v)) was 51.4 ± 0.50 g/L. The produced pullulan had an average molecular weight (M w ) of 2.07 × 10 5  g.mol -1 based on gel permeation chromatography results. The decomposition temperature (T d ) of the produced pullulan was ~300 °C and also, the resulting pullulan had a Newtonian flow behavior in a wide range of concentrations., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Various (semi)-synthetic non-digestible glucans (NDG) (resistant (malto)dextrin, isomaltooligosaccharide, soluble corn fiber, polydextrose) were analyzed by methylation analysis, 1 H NMR spectroscopy, ESI-MS n , TLC, and capillary electrophoresis (CE/UV). Partly complementary and partly corroborative results were obtained by these methods yielding a comprehensive overview about the various degrees of complexity and special structural features. Methylation analysis enabled the most detailed quantitative evaluation of glycosidic linkage positions and branching pattern, and detection of furanosyl residues. 1 H NMR spectroscopy provided additional information on anomeric configuration. By ESI-IT-MS up to DP 13, for doubly charged up to DP 22 was detected. Glucitol residues in polydextrose as well as anhydrosugar formation in thermally treated glucans could also be recognized from the mass spectra. Furthermore, MS 2 of the disaccharide portion gave insights into the linkage positions present in the glucan mixture. Electrophoresis of ANTS-labeled oligosaccharides showed the DP-resolved differences of complexity and was the most powerful method to identify the type of glucan by its CE-fingerprint. The aim was to present complementary analytical data obtained by application of identical conditions and methods to a wide range of NDG with increasing complexity to allow direct structure comparison., Competing Interests: Declaration of competing interest The authors gratefully acknowledge financial support for this project from Beneo GmbH, Germany, which had no role in the study design, data collection, analysis, interpretation or manuscript preparation. This financial support did not confine the authors from publishing their results. Publishing this research was possible without the prior approval of the sponsor. The authors declare no competing financial interest., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Mixtures of partially O-methylated alditol acetate standards of galactofuranose were synthesized rapidly. Methyl galactofuranosides were obtained with a yield of 79.9% within 4h under optimized reaction conditions. Methylation of methyl glycosides was carried out in the presence of BaO/Ba(OH)2·8H2O, giving rise to mixtures of partially methylated glycosides. The batch containing the most diverse structures of methyl ethers was converted into partially O-methylated alditol acetates (PMAAs) and then subjected to GC-MS. These PMAAs could be used as GC-MS standards for simultaneous identification of galactofuranose units with diverse linkages in complex carbohydrates., (Copyright © 2013 Elsevier Ltd. All rights reserved.)